Alma Mater Studiorum Universit`a degli studi di Bologna Computational modelling of human stem ...

192 Pages·2013·5.5 MB·English

Alma Mater Studiorum
Universita` degli studi di Bologna
Department of Electrical, Electronic
and Information Engineering “Guglielmo Marconi”
Scuola di Dottorato in Bioingegneria - Ciclo XXV
Settore concorsuale di afferenza: 09/G2
Settore scientifico disciplinare di afferenza: ING-INF/06
Computational modelling of human stem
cell-derived cardiomyocytes
-
Texture descriptors for biological image
processing
presented by
Michelangelo Paci
Supervisor Co-supervisor
Prof. Gianni Gnudi Prof. Stefano Severi
Reviewers Ph.D. Coordinator
Prof. Claudio Lamberti Prof. Angelo Cappello
Prof. Cristiana Corsi
Prof. Beatriz Tre´nor
Year 2013, Final Exam

KEYWORDS
Cardiomyocytes
Computational models
Human embryonic stem cells
Human induced pluripotent stem cells
Current blockers
-
Image classification
Texture descriptors
3

ACRONYMS
I inward rectifier K+ current
K1
I Na+ current
Na
I rapid delayed rectifier K+ current
Kr
I slow delayed rectifier K+ current
Ks
I L-type Ca2+ current
CaL
I T-type Ca2+ current
CaT
I transient outward K+ current
to
I funny current
f
I Na+ /K+ pump
NaK
I Na+ /Ca2+ exchanger
NaCa
I sarcolemmal Ca2+ -ATPase
pCa
I Background Ca2+ current
bCa
I Sarcoplasmic Reticulum (SR) uptake current
up
I SR release current
rel
I SR leakage current
leak
I Stimulus current
stim
5
6 Acronyms
AP Action Potential
APA Action Potential Amplitude
APD Action Potential Duration
APD APD at 10% of repolarization
10
APD APD at 30% of repolarization
30
APD APD at 40% of repolarization
40
APD APD at 50% of repolarization
50
APD APD at 70% of repolarization
70
APD APD at 80% of repolarization
80
APD APD at 90% of repolarization
90
CaMK Ca2+/calmodulin-dependent protein kinase II
Chr 3R4S-Chromanol 293B
CM cardiomyocyte
Cm Membrane capacitance
DDR Diastolic Depolarization Rate
EAD Early After Depolarization
EB Embryod Body
EC excitation/contraction
F Rate of spontaneous beating
hESC human embryonic stem cell
hiPSC human induced pluripotent stem cell
hESC-CM human embryonic stem cell-derived cardiomyocyte
hiPSC-CM human induced pluripotent stem cell-derived cardiomyocyte
Michelangelo Paci
Acronyms 7
LQTS Long QT Syndrome
MDP Maximum Diastolic Potential
Nifed Nifedipine
ORd O’Hara - Rudy
Peak Peak Voltage
SR Sarcoplasmic Reticulum
TTX Tetrodotoxine
V Cell volume
c
V Maximum Upstroke Velocity
max
V Ca2+ transient Maximum Upstroke Velocity
maxCa,upstroke
V Ca2+ transient Maximum Decay Velocity
maxCa,decay
V Sarcoplasmic Reticulum volume
SR
ANA Antibody Antinucleus
ASM Angular Second Moment
AUC area under the ROC curve
FUSr fusion by sum rule between MLQPr and MLPQ3
FUSu fusion by sum rule between MLQPu and MLPQ3
GLCM Grey Level Co-occurence Matrix
HAR Haralick features
IIF Indirect Immunofluorescence
L(3) LPQ with radius = 3 pixels
L(5) LPQ with radius = 5 pixels
L(3+5) concatenation of the bins extracted by L(3) and L(5)
Ph.D. Thesis
8 Acronyms
LBP Local Binary Pattern
LE Locate Endogenous
LPQ3 single LPQ with ternary coding
LPQ Local Phase Quantization
LPQ3 LPQ with ternary coding
LQP Local Quinary Pattern
LQPu LQP with uniform mapping
LT Locate Transfected
LTPu single LTP with uniform mapping
LTP Local Ternary Pattern
MLPQ3 Multi-Threshold LPQ3
MLQP Multi-Threshold LQP
MLQPr Multi-Threshold LQP with rotation invariant uniform mapping
MLQPu Multi-Threshold LQP with uniform mapping
MLTPu Multi-Threshold LTP with uniform mapping
RU(8) rotation invariant uniform bins extracted using LBP with radius =
8 pixels
RU(16) rotation invariant uniform bins extracted using LBP with radius =
16 pixels
RU(8+16) concatenation of the bins extracted by RU(8) and RU(16)
STFT Short Term Fourier Transform
SVM Support Vector Machine
U(8) uniform bins extracted using LBP with radius = 8 pixels
U(16) uniform bins extracted using LBP with radius = 16 pixels
Michelangelo Paci
Acronyms 9
U(8+16) concatenation of the bins extracted by U(8) and U(16)
VE Methods to compute the LTP proposed by V´escei at al. in Comput
Bio Med 2011; 41(6): 313-25.
VLQ VE method applied to LQP
MV1 VE variant where a different threshold is calculated for each class
in each dataset
Ph.D. Thesis